rs142375882
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 1P and 9B. PP2BP4_StrongBP6BS2
The NM_006258.4(PRKG1):c.2014G>A(p.Asp672Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000527 in 1,613,098 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. D672D) has been classified as Likely benign.
Frequency
Consequence
NM_006258.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRKG1 | NM_006258.4 | c.2014G>A | p.Asp672Asn | missense_variant | 18/18 | ENST00000373980.11 | |
PRKG1 | NM_001098512.3 | c.1969G>A | p.Asp657Asn | missense_variant | 18/18 | ||
PRKG1 | NM_001374781.1 | c.805G>A | p.Asp269Asn | missense_variant | 14/14 | ||
PRKG1 | XM_017016413.2 | c.1711G>A | p.Asp571Asn | missense_variant | 18/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRKG1 | ENST00000373980.11 | c.2014G>A | p.Asp672Asn | missense_variant | 18/18 | 1 | NM_006258.4 | ||
PRKG1-AS1 | ENST00000452247.7 | n.461+62C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000592 AC: 9AN: 152110Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000159 AC: 40AN: 250922Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135586
GnomAD4 exome AF: 0.0000520 AC: 76AN: 1460988Hom.: 0 Cov.: 30 AF XY: 0.0000440 AC XY: 32AN XY: 726790
GnomAD4 genome ? AF: 0.0000592 AC: 9AN: 152110Hom.: 0 Cov.: 31 AF XY: 0.0000404 AC XY: 3AN XY: 74300
ClinVar
Submissions by phenotype
Familial thoracic aortic aneurysm and aortic dissection Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 18, 2022 | The c.2014G>A (p.D672N) alteration is located in exon 18 (coding exon 18) of the PRKG1 gene. This alteration results from a G to A substitution at nucleotide position 2014, causing the aspartic acid (D) at amino acid position 672 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Apr 01, 2022 | Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports that this missense variant has a deleterious effect on protein structure/function - |
Aortic aneurysm, familial thoracic 8 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 30, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at